On 2013-06-06 22:13, Geoffrey Hutchison wrote:
Although I'm starting to think that json is such a simple format
that
it could do without a strict chemical specification. Getting json out of
an OBMol is 5 lines of code
My concern is the opposite. It's always easy to write to an
arbitrary
Regarding using JSON as a new file format...
This discussion has focussed on the syntax of JSON, but completely
overlooks the real problem with ALL chemical file formats: how do you
handle all of the cases where a simple connection-table (ball and stick)
doesn't capture reality? Things like
On Thu, Jun 6, 2013 at 2:11 PM, Patrick Fuller patrickful...@gmail.comwrote:
Tim,
I think Dimitri's point is that all the references are implicitly defined
by list indices, rather than explicit keys. For example, something like
{
atoms: {
C1: { element: C, location: [
If you're going to rely on positions within arrays, why not just do it the
simple way?
{ smiles: [CCO],
2D: [1,1,2,2,3,3],
3D: [1,1,1,2,2,2,3,3,3]
}
Smiles are a great representation of molecules (especially with
smarts/smirks regex), and, in cases where they can be used, I think they're
the
On 06/07/2013 12:25 PM, Patrick Fuller wrote:
Geoff - Outside of some fairly minor issues, xml translates easily to json.
Could the chemical xml specification just be translated to json?
If you gloss over things like #[P]CDATA, (elt+), (#CDATA|(foo,bar,baz)),
it's trivial. Except for
I don't think we need to worry about the naming conventions of corner cases
just yet. Taking something basic, ethane in cml
molecule
atomArray
atom id=a1 elementType=C x3=0.229656 y3=0.720147 z3=-0.015085/
atom id=a2 elementType=C x3=-0.229656 y3=-0.720147 z3=0.015085/
/atomArray
bondArray
On Fri, Jun 7, 2013 at 10:25 AM, Patrick Fuller patrickful...@gmail.comwrote:
A SMILES contains exactly the same information as the atom/bond lists in a
much more compact form. If you want to avoid the aromaticity problem, just
use Kekule form, which makes it virtually identical to any other
Wow, that was a very insightful email. Thank you for writing it.
Getting back to something actionable, what do you think about the idea of
just translating the CML standard to json? Outside of some nuances, XML and
JSON generally accomplish the same thing, so I would think that the
chemical XML
On 06/07/2013 01:45 PM, Craig James wrote:
... The CML project is one such (you might
want to look at it for ideas), but it never got traction.
XML is bad at tabular data. A table of x, y, x coordinates in properly
formatted xml is at least twice as many bytes (x123.456/x uses as
many bytes
Hi,
I think CML is definitely a useful starting point, however I think it would be
a mistake to just translate everything across in a literal way. In particular,
I think it's definitely worth thinking carefully about the different strengths
of the XML and JSON formats (in both syntax and
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